Abstract
Low temperature significantly affects rice growth and yield. Temperatures lower than 15°C are generally detrimental for germination and uniform seedling stand. To investigate the genetic architecture underlying cold tolerance during germination in rice, we conducted a genome-wide association study using a novel diversity panel of 257 rice accessions from around the world and the 7K SNP marker array. Phenotyping was conducted in controlled growth chambers under dark conditions at 13°C. The rice accessions were measured for low-temperature germinability, germination index, coleoptile length under cold stress, plumule length at 4-day recovery, and plumule length recovery rate. A total of 51 QTLs were identified at p < 0.001 and 17 QTLs were identified using an FDR < 0.05 across the different chilling indices with the whole panel of accessions. At the threshold of p < 0.001, a total of 20 QTLs were identified in the subset of japonica accessions, while 9 QTLs were identified in the subset of indica accessions. Considering the recurring SNPs and linked SNPs across different chilling indices, we identified 31 distinct QTL regions in the whole panel, 13 QTL regions in the japonica subset, and 7 distinct QTL regions in the indica subset. Among these QTL regions, three regions were common between the whole panel and japonica, three regions were common between the whole panel and indica, and one region was common between indica and japonica. A subset of QTL regions was potentially colocalized with previously identified genes and QTLs, including 10 from the japonica subset, 4 from the indica subset, and 6 from the whole panel. On the other hand, a total of 21 potentially novel QTL regions from the whole panel, 10 from the japonica subset, and 1 from the indica subset were identified. The results of our study provide useful information on the genetic architecture underlying cold tolerance during germination in rice, which in turn can be used for further molecular study and crop improvement for low-temperature stressed environments.
Highlights
Rice is more susceptible to cold stress than other cereal crops due to its origin in the tropical and subtropical regions (Zhao et al, 2017)
Among the 31 unique QTL regions (p < 0.001) associated with chilling indices of the whole set of accessions, we identify 10 loci potentially co-localized with the previously identified genes/ QTLs related to cold stress in rice, including cold tolerance during germination, seedling and reproductive stage, and cold recovery (Table 4; Supplementary Table 2)
The separate GWAS analysis of low-temperature germinability (LTG) and germination index (GI) helped us to discover whether the chilling tolerance was due to the inherent cold tolerance ability or due to high seedling vigor
Summary
Rice is more susceptible to cold stress than other cereal crops due to its origin in the tropical and subtropical regions (Zhao et al, 2017). One of the major challenges for rice production under direct-seeded cultivation, especially in high altitude regions in the tropics or regions with temperate climates, is low-temperature sensitivity during the germination stage (Schläppi et al, 2017). Cold stress during germination causes poor germination and retarded plant growth. Breeding of rice cultivars with tolerance of low temperature, has been challenging due to various factors: response of rice plants to cold varies with growth stages (Liu et al, 2015); low-temperature tolerance is controlled by quantitative loci where many genes with small effects contributing to the phenotype (Ji et al, 2009); and epistatic interaction among alleles at unlinked loci (Zhang et al, 2014a). A few studies have been performed to improve cold tolerance of the indica cultivars using japonica cultivars; due to lack of genetic diversity in japonica germplasm, further improvement of japonica cultivars has been quite challenging (Zhang et al, 2014a)
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